A phylogenomic gene cluster resource: The phylogeneticallyinferred groups (PhlGs) database

Journal Article · Thu Aug 25 04:00:00 EDT 2005 · BMC Bioinformatics, Biomed Central

OSTI ID:882266

Dehal, Paramvir S; Boore, Jeffrey L

We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community.

• Research Organization: Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE Director, Office of Science. Office of Biological andEnvironmental Research; National Science Foundation
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 882266
• Report Number(s): LBNL--59016; BnR: 600305000
• Journal Information: BMC Bioinformatics, Biomed Central, Journal Name: BMC Bioinformatics, Biomed Central Vol. 7
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
BIOLOGICAL EVOLUTION
GENES
Genomics Phylogenomics evolution gene function gene familyannotation
INFORMATION SYSTEMS